http://5pointsfitness.com/
I trained there for a while. Good Muay Thai, and the people you will train with will in general be bigger and better than you. But they're also nice guys so they'll help you learn. Good kali instruction as well, and Simon is a great guy and teacher. You'll get a lot of time to work with him in the kali classes b/c they're generally smaller. They even offer BJJonce a week, when they bring in a grappling instructor.
Pretty easy to get to by either the R or E lines from Queens. Pricey, but IMO worth it.
http://www.thewat.com/enter.html
This place had more of a sport Muay Thai oriented focus. I didn't train there but I know guys who've trained under Phil Nurse and they turned out pretty damn good. I did check it out though and it looked like a nice place, very clean, good equipment.